Programmable endonucleases have increasingly become an important tool for targeted genome engineering or modification in eukaryotes. Recently, RNA-guided clustered regularly interspersed short palindromic repeats (CRISPR) systems have emerged as a new generation of genome modification tools. These new programmable endonucleases provide unprecedented simplicity and versatility as compared to previous generations of nucleases such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). However, chromatin barriers in eukaryotic cells can hinder target access and cleavage by the prokaryote-derived CRISPR systems (Hinz et al., Biochemistry, 2015, 54:7063-66; Horlbeck et al., eLife, 2016, 5:e12677).
In fact, no or low editing activity on certain mammalian genomic sites has been observed when using Streptococcus pyogenes Cas9 (SpCas9), which is considered the most active CRISPR nuclease to date. Moreover, many of the CRISPR nucleases that have been characterized thus far exhibit no activity in mammalian cells, even though they are active in bacteria or on purified DNA substrates. Therefore, there is a need to improve the ability of CRISPR nuclease systems and other programmable DNA modification proteins to overcome chromatin hindrance to increase the efficiency of targeted genome or epigenetic modification in eukaryotes.